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Biochemistry and Biomolecules

Refresh your knowledge with a chemistry refresher integrated into physiology. Learn about atoms, periodic table trends, bonding types, and key interactions in biochemistry. Understand how chemistry works in biological models and the composition of matter.

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Biochemistry and Biomolecules

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  1. Biochemistry and Biomolecules

  2. Today • A little chemistry refresher • Classes of Biomolecules • Integrated into Physiology

  3. Chemistry Refresher • Chemistry: • the science concerned with the composition, behavior, structure, and properties of matter, as well as the changes it undergoes during chemical reactions • Biochemistry: • how chemistry works in biological models • i.e. protein assemblages

  4. Chemistry Refresher • Composition of Matter = Atom • the configuration of the atom will determine the properties of matter • atoms are composed of • positively charged core (nucleus) composed of • protons (charged) • neutrons (neutral) • negatively charged electrons • number of which is determined by the nuclear charge • arranged in electron shells • determines “activeness” or reactivity of the atom e- e- + e- + + + e- + + e- e-

  5. a = mass number (protons + neutrons) atomic charge atomic symbol C X z = atomic number (no. of protons) Chemistry Refresher • atomic notation +- a 12.011 z 6

  6. Chemistry Refresher • Atomic number • The number of protons = the number of electrons • Number of electrons in the outer shell determines stability and atoms ability to • gain additional electrons • lose electrons • This gain/loss of electrons is accomplished by donating, accepting or sharing electrons

  7. C Chemistry Refresher • Periodic Table • contains a listing of all of the elements • notation is slightly different from the standard atomic notation standard atomic notation periodic table notation 6 12.011 carbon C 6 12.011

  8. Chemistry Refresher • Periodic Table Period & Group Trends • Periods (horizontal) • Number indicates the number of electron shells • Period 1 = one electron shell (H & He only) • Left to right • atomic radius decreases • atomic ionization energy increases (becomes more difficult to remove an electron) • Electron affinity increases (with the exception of the noble gases on the far right) • Groups (vertical) • From top to bottom • the atomic radius increases • The atomic ionization energy decreases (electrons that are farther away from the nucleus are less tightly held) • Electronegativity decreases from top to bottom

  9. Chemistry Refresher • Periodic Table Periods & Groups • Groups (vertical) • Determined by the number of valence shell electrons • Valence shell is just the outermost electron shell • From top to bottom • the atomic radius increases • The atomic ionization energy decreases (electrons that are farther away from the nucleus are less tightly held) • Electronegativity decreases from top to bottom

  10. Chemistry Refresher • So… valence shell electrons are critical! • Stability is desired and achieved by • Donating & Accepting electrons • forms ionic bonds • Sharing electrons • forms covalent bonds • Electrostatic forces • weaker hydrogen bonds and van der waals interactions

  11. Chemistry Refresher • Ionic Bonding • One atom donates electrons and the other receives them forming charged ions • Charged ions are electrostatically attracted to each other and so form a bond. • Example: NaCl • Sodium has 1 electron in its outer shell • Chlorine has 7 electrons in its outer shell • Upon contact, sodium gives up its one electron and • Na becomes a positively charged ion • Cl becomes a negatively charged ion • and…. e- e- e- e- e- Na e- + e- e- e- e- e- e- e- e- e- e- e- Cl e- - e- e- e- e- e- e- e- e- e- e- e-

  12. Chemistry Refresher • Covalent Bonding • Electrons are shared • For each pair that is shared a single bond is formed • For each two pair that are shared a double bond is formed • For each three pair that are shared a triple bond is formed • Covalent bonds can form • Non-polar bonds (when electrons are shared equally) • Ex. Methane (CH4) • Polar bonds (when electrons are shared unequally) • Ex. Water (H2O) • Extensive bonding can result in larger molecules that have both polar and non-polar regions = amphipathic molecules • Ex. Phospholipids

  13. Chemistry Refresher H + + H H e- e- e- e- C O H H e- e- e- e- e- e- e- e- e- e- e- H e- - Non-Polar Molecule (Methane – CH4) Polar Molecule (Water – H2O)

  14. Chemistry Refresher Phospholipid Amphipathic Molecule

  15. Chemistry Refresher • Other important interactions • Hydrogen bond • A covalently bound hydrogen interacts with a nearby electronegative atom of O,N or Fl • Weaker than covalent bonds • Why is it important? • Aids in protein configuration (secondary, tertiary & quaternary) • Creates surface tension of water • Van der Waals interaction • Weak attractive or repulsive electrostatic forces between molecules or parts of molecules • Weaker than hydrogen bonds but still responsible for aiding in protein configuration

  16. Biomolecules • Any organic molecule that is produced, used or functioning in a biological organism • Have in common • All have at least: carbon, hydrogen, oxygen • Also commonly found are nitrogen, phosphorous • What don’t they have in common? • Shape! • Why? • Different order, amount, bonding… • Classes of Biomolecules • Nucleosides (nucleotides) • Saccharides (carbohydrates) • Amino Acids (proteins) • Lipids

  17. H HOCH2 O HO HO CH2OH OH Biomolecules • Carbohydrates • General formula = (CH2O)n • Simple surgars • monomer units = monosaccharides (n = 6) • fructose • glucose • Galactose • Dimer units = disaccharides (n=12) • Sucrose • Maltose • Lactose • Multiple units = polysaccharides • Glycogen – we produce • Starch – we consume and use • Cellulose – we consume & …

  18. Biomolecules • How does a monomer become a dimer or polymer? • Dehydration synthesis (condensation reaction) CH2OH H O HOCH2 H O glucose HO fructose HO HO OH H O CH2OH OH OH H2O + This is a anabolic reaction

  19. Biomolecules • How does a polymer get broken down? • Through hydrolysis reactions CH2OH H O HOCH2 H O glucose HO fructose O HO HO OH H CH2OH OH OH H2O + This is a catabolic reaction

  20. Biomolecules • The functional importance of carbohydrates • Good for storage of energy (glycogen) • Used in production of ATP • Provides dietary fiber (cellulose) • Used in conjunction with lipids and proteins in membrane physiology • Ribose forms (along with phosphate) the backbone of DNA

  21. Biomolecules • Lipids (fats) • Consist of • glycerol backbone (3 carbons) • Hydrocarbon tails • Number of tails • 1 = monoglycerides • 2 = diglycerides • 3 = triglycerides (90% of lipids in this form in us) • Determine nature of lipid by the bonding present • No double bonds = saturated • Double bonds = unsaturated (mono or poly) • Significance?

  22. triglyceride glycerol Fatty acid chains saturated or unsaturated?

  23. Biomolecules • Phospholipids – major lipid-related molecule • Major component of cell membrane • One fatty acid is replaced by a polar phosphate group which creates • a hydrophillic “head” region • a hydrophobic “tail” region

  24. Biomolecules • Other Lipid-Related Molecules • Eicosanoids • Four important families of compounds derived from eicosanoids: • Prostaglandins – wide range of functions (cell growth to pain) • Prostacyclins – antagonistic to thromboxane, vasodilator • Leukotrienes – sustain inflammatory reactions in allergies & asthma • Thromboxanes – involved in platelet plug formation • Derived from omega-3 and omega-6 essential fatty acids • Levels determine health in these main areas • Cardiovascular • Arthritis • Triglyceride levels • Blood pressure

  25. Biomolecules • Other Lipid-Related Molecules • Steroids • Created from cholesterol in human physiology • Four linked carbon rings with a carbon tail • Wide range of function from cell membranes to human growth H CH3 H C CH3 C CH2 CH2 CH2 CH3 CH3 CH3 cholesterol HO

  26. Biomolecules • Proteins • Proteins are polymers of amino acids • Extremely versatile due to the different R (reactive) groups that allow for • 20 different amino acids • 11 are “non-essential” • 9 are “essential” • Unlimited arrangement of amino acids • Unlimited shapes due to molecular forces between molecules and steric strain (Van der Waals repulsion) due to the structural makeup of the R groups as well as di-sulfide bonds and hydrogen bonds

  27. Biomolecules • Amino Acid Structure reactive group acid end H R O amine end H N C C H O H How is a protein made from an amino acid?

  28. Biomolecules • Protein Production • Amino acids joined together by dehydration synthesis, forming a peptide bond • OH from the acid end • H from the amine end H2O H H R R O O H H N C C N C C H H O O H H

  29. H O H Dipeptide + Water H R R O H N N C C C C H O H H H O

  30. H H R R R R O O H H N N N N C C C C C C C C H H O O H H H H H H O O Bending of Amino Acids • Depending on the R groups, the amino acids may bend toward or away from each other

  31. Biomolecules • Protein Production Sequence • Initial chain of amino acids from translation is the primary protein • Folding or bending into sheets, or helices forms secondary proteins • Configuring into a globular three dimensional shape is a tertiary protein • More than one tertiary protein combining forms a quaternary protein

  32. Biomolecules • Sequence ofprotein formation

  33. Biomolecules • Proteins – why do we care? • Found in all cells • Acting as transporters, movers, enzymes, regulators • Within and on the cell • Establishes membrane potential • Provides cytoskeletal materials • Some gets exported from the cell to support extracellular matrix • Functions in cell to cell adhesion/communication • Mediate extracellular reactions • Act as signal molecules and hormones/neurotransmitters • Provide movement and structure • Provide raw material for new protein production • Defense in immunoglobulin production

  34. Biomolecules • Proteins can form bonds with other biomolecules • Lipoproteins • glycoproteins

  35. Biomolecules • Nucleotides • Composed of • Phosphate group (s) • 5 carbon sugars • May be ribose or deoxyribose • Nitrogenous base • One of two types of carbon-nitrogen ring structure • Purines – double ring (guanine & adenine) • Pyrimidines – single ring (cytosine, thymine & uracil)

  36. Biomolecules • Nucleotides form • Informational structures • DNA and RNA • Energy Structures • ATP, ADP, FAD, NAD, GTP, GDP • Messengers • Cyclic AMP • Cyclic GMP

  37. Biochemistry • Biomolecule reactions • We already know bonding, dehydration and hydrolysis reactions • Need to know: • Reaction directions, rates & enzyme function • Solutions • pH & buffers Lab Next Week!

  38. Integrated Physiology • Biomolecules give us an understanding of why particular structures are capable of doing what they do! • They play a role in every aspect of physiology.

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